DNA Structure

Relatively simple topic for this post- should be my last one tonight.

List hypotheses on the origin of life on earth.

There are many different hypotheses for the origin of life on Earth, but only four were covered in the course.

#1: Organic chemical synthesis in a reducing atmosphere. It was thought that the Earth originally had a reducing atmosphere, in which hydrogen and methane gases were abundant. The significance of this is that it has also been found that hydrogen, methane and ammonia can form a "prebiotic soup" made of amino acids and nucleotides when exposed to water and electrical discharges. However, the current consensus is that the primitive atmosphere was not reducing. It is also unclear how membrane-enclosed cells could have formed.

#2: Carriage by meteorites/comets. Part of the evidence behind this hypothesis is the abundance of organic compounds found in space. The issue with this hypothesis, however, is that it simply changes the question to "How did life originate in space?"

#3: Synthesis on metal sulfides in deep sea vents. Apparently vents are sites of abundant biological activity that can form prebiotic soups similar to those mentioned in #1 (well, that's my understanding anyway). The prebiotic soup here can self-organise on a metal sulfide surface. Once again, however, the question of how membrane-enclosed cells are formed is raised.

#4: RNA World. This hypothesis suggests that RNA may have been the first living, self-replicating entity. Some RNA is capable of storing information and/or catalysing reactions. Yet again, the question is raised of how membrane-enclosed cells are formed.

Know the main events which led to the discovery of DNA.

Watson and Crick are the two scientists mostly credited for the discovery of the structure of DNA, but there were also several others who contributed towards their discovery. Watson and Crick worked together in the same laboratory. Watson was first shown an X-ray diffraction image of DNA by Maurice Wilkins at a conference. Later on, Rosalind Franklin produced an even better image. This data allowed Watson and Crick to propose their first model of DNA, which was a three-stranded model.

This model, as I'm sure you know, was found to be incorrect. It was also inconsistent with Franklin's data, as she pointed out to the pair. The next year, Watson and Crick were visited by Edwin Chargaff, who showed them his data about the ratio of A/T and G/C in DNA, thus providing another small piece of the puzzle. Yet more data was obtained from later X-ray diffraction data taken by Wilkins.

Eventually, in 1953, Watson and Crick used all of the information that they had gathered to produce a double-stranded helical model of DNA. Apparently, after they had their "Eureka!" moment, they went to the local pub to announce that they had found out the secret of life. (I wonder how many weird looks they got for that?) Watson, Crick and Wilkins all obtained the Nobel Prize. Unfortunately, Franklin did not receive the Nobel Prize, as she had died of ovarian cancer before the prize was awarded, and you cannot receive a Nobel Prize posthumously.

Be able to describe the main features of DNA.

DNA is made up of two antiparallel strands of nucleotides. Each nucleotide is made up of deoxyribose sugar, which is bound to a base at the 1' carbon and a phosphate group at the 5' carbon. The bases on the two strands are hydrogen bonded to each other, with adenine pairing to thymine and cytosine pairing with guanine. The two strands are wound around into a right-handed double helical structure.

Understand how the genetic code works.

Messenger RNA has series of "codons." Each codon is three bases long and codes for one amino acid. The genetic code is degenerate, which means that several different codons can all code for the same amino acid. There are also three codons that are "stop" codons- that is, instead of coding for an amino acid, they bind release factors which cause the ribosome to release the polypeptide.

Know what is meant by “the central dogma.”

The central dogma is simply the process in which DNA is transcribed into mRNA, which is then translated into protein.

Know the terminology for bases, nucleotides, nucleosides, deoxy, ribo.

There are several different bases present in RNA and DNA. These include adenine, thymine, cytosine, guanine and uracil. (There are other modified bases, but they're not important to us at this stage.)

When these bases are bound to a sugar (ribose or deoxyribose), they form a nucleoside. These nucleosides are called adenosine, thymidine, cytidine, guanosine and uridine. (I'm sure you can guess which nucleoside contains which base.)

A nucleotide is a nucleoside bound to one or more phosphates. For naming, you take the nucleoside name and then "monophosphate" or "diphosphate" or whatever-phosphate. For example, adenosine with three phosphate groups bound is adenosine triphosphate- otherwise known as ATP, an energy carrier in the cell.

If you want to be really precise, you can also add deoxy- or ribo- prefixes to nucleoside and nucleotide names in order to make it clear whether the sugar is deoxyribose or ribose, respectively.

Be able to define the terms antiparallel, complementary base pairing, coding strand, codon, right-handed helix, major groove.

Antiparallel- The two strands are parallel to each other, but run in opposite directions.
Complementary base pairing- Bases bind to complementary bases: adenine always pairs with thymine (in DNA) or uracil (in RNA) and cytosine always pairs with guanine.
Coding strand- The strand opposite to the template strand. (The template strand is the one that is copied off during the process of transcription.)
Codon- A series of three bases on the mRNA. Each codon codes for an amino acid (except for the three stop codons, which cause release factors to bind). Multiple codons may code for the same amino acid.
Right-handed helix- A clockwise helical structure.
Major groove- A relatively large groove in the side of the DNA helix.